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https://compbio.dfci.harvard.edu/predictivenetworks//

A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model.

Proper citation: Predictive Networks (RRID:SCR_006110) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/pubmed/

Public bibliographic database that provides access to citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. PubMed citations and abstracts include fields of biomedicine and health, covering portions of life sciences, behavioral sciences, chemical sciences, and bioengineering. Provides access to additional relevant web sites and links to other NCBI molecular biology resources. Publishers of journals can submit their citations to NCBI and then provide access to full-text of articles at journal web sites using LinkOut.

Proper citation: PubMed (RRID:SCR_004846) Copy   

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http://www.cbcb.umd.edu/software/phymm/

Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy.

Proper citation: Phymm and PhymmBL (RRID:SCR_004751) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/sra

Repository of raw sequencing data from next generation of sequencing platforms including including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. In addition to raw sequence data, SRA now stores alignment information in form of read placements on reference sequence. Data submissions are welcome. Archive of high throughput sequencing data,part of international partnership of archives (INSDC) at NCBI, European Bioinformatics Institute and DNA Database of Japan. Data submitted to any of this three organizations are shared among them.

Proper citation: NCBI Sequence Read Archive (SRA) (RRID:SCR_004891) Copy   

•   Source: SciCrunch Registry

http://pdbml.pdb.org/

Markup Language that provides a representation of PDB data in XML format. The description of this format is provided in XML schema of the PDB Exchange Data Dictionary. This schema is produced by direct translation of the mmCIF format PDB Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below. * PDBML data files are provided in three forms: ** fully marked-up files, ** files without atom records ** files with a more space efficient encoding of atom records * Data files in PDBML format can be downloaded from the RCSB PDB website or by ftp. * Software tools for manipulating PDB data in XML format are available.

Proper citation: Protein Data Bank Markup Language (RRID:SCR_005085) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/sim4cc/

Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species.

Proper citation: sim4cc (RRID:SCR_001204) Copy   

•   Source: SciCrunch Registry

http://www.findmice.org/index.jsp

Database of mouse strains and stocks available worldwide, that will assist international research community in finding mouse resources they need, including inbred, mutant, and genetically engineered mice. IMSR is multi institutional international collaboration supporting use of mouse as model system for studying human biology and disease. IMSR began with initial collaboration between Mouse Genome Informatics (MGI) group at Jackson Laboratory and Medical Research Council Mammalian Genetics Unit at Harwell. Additional institutions and collaborators are now contributing mouse resource information to IMSR. Data content found in IMSR is as it was supplied by data provider sites. You are encouraged to participate in making this database as complete as possible for all worldwide mouse strain resources. If you or your institution hold mice, cryopreserved gametes or embryos, or ES cell lines that you distribute to other researchers, contributing information about them to IMSR catalog will make them more widely known.

Proper citation: International Mouse Strain Resource (RRID:SCR_001526) Copy   

•   Source: SciCrunch Registry

http://globin.cse.psu.edu/

Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles.

Proper citation: Globin Gene Server (RRID:SCR_001480) Copy   

•   Source: SciCrunch Registry

https://pdbp.ninds.nih.gov

Common data management resource and web portal to promote discovery of Parkinson's Disease diagnostic and progression biomarker candidates for early detection and measurement of disease progression. PDBP will serve as multi-faceted platform for integrating existing biomarker efforts, standardizing data collection and management across these efforts, accelerating discovery of new biomarkers, and fostering and expanding collaborative opportunities for all stakeholders.

Proper citation: Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) (RRID:SCR_002517) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/gap

Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits.

Proper citation: NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/Genbank/

NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.

Proper citation: GenBank (RRID:SCR_002760) Copy   

•   Source: SciCrunch Registry

http://sumsdb.wustl.edu/sums/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures

Proper citation: SumsDB (RRID:SCR_002759) Copy   

•   Source: SciCrunch Registry

http://druginfo.nlm.nih.gov/drugportal/drugportal.jsp

The NLM Drug Information Portal gives users a gateway to selected drug information from the U.S. National Library of Medicine and other key U.S. Government agencies. At the top of the page are links to individual resources with potential drug information, including summaries tailored to various audiences. Resources include the NLM search systems useful in searching for a drug, NLM research resources, resources organized by audience and class, and other NIH and government resources such as FDA and CDC. The search box in the middle of the page lets you search many of these resources simultaneously. More than 34,000 drugs can be searched using this facility. The portal covers drugs from the time they are entered into clinical trials (Clinicaltrials.gov) through their entry in the U.S. market place (Drugs@FDA). Many drugs in other countries are covered, but not as thoroughly as U.S. drugs. The PubMed link provides medical literature describing research, and TOXLINE provides toxicology literature. Resources such as MedlinePlus provide easy to read summaries of the uses and efficacy of a drug. You may search by a drug's trade name or generic name. For example, the trade name Advil and the generic name ibuprofen will retrieve the same drug record. As you type in a name, suggestions are given beneath the search box. A spell checker gives suggestions if the name is not found. You can find embedded portions of names by using an asterisk at the beginning and/or end of a search term. You can also search by the general Category of usage of a drug by checking that radio button. Suggestions are given as you type here too. Once a drug is found, a summary of the drug's type and usage is given, as well as links leading to further information at one of the portal's resources. Outside links open in a new window. Within a given drug record, you may click on the drug category and retrieve drugs with the same or similar uses. * View drug category descriptions. * View top By Name searches (previous seven days). * View top By Category searches (previous seven days). * View top dispensed prescriptions in the US Market, 2010. * View common drug name list. * View category name list. * View list of resources searched. JavaScript must be enabled in your browser for the NLM Drug Information Portal to work properly.

Proper citation: Drug Information Portal (RRID:SCR_002818) Copy   

•   Source: SciCrunch Registry

http://www.rostlab.org/cms/

A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research.

Proper citation: ROSTLAB (RRID:SCR_000792) Copy   

•   Source: SciCrunch Registry

http://ligand-expo.rutgers.edu/

An integrated data resource for finding chemical and structural information about small molecules bound to proteins and nucleic acids within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components.

Proper citation: Ligand Expo (RRID:SCR_006636) Copy   

•   Source: SciCrunch Registry

https://wiki.nci.nih.gov/display/LexEVS/LexGrid

LexGrid (Lexical Grid) provides support for a distributed network of lexical resources such as terminologies and ontologies via standards-based tools, storage formats, and access/update mechanisms. The Lexical Grid Vision is for a distributed network of terminological resources. It is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services, and can parse OBO format, as well as other formats such as OWL. Currently, there are many terminologies and ontologies in existence. Just about every terminology has its own format, its own set of tools, and its own update mechanisms. The only thing that most of these pieces have in common with each other is their incompatibility. This makes it very hard to use these resources to their full potential. We have designed the Lexical Grid as a way to bridge terminologies and ontologies with a common set of tools, formats and update mechanisms. The Lexical Grid is: * accessible through a set of common APIs * joined through shared indices * online accessible * downloadable * loosely coupled * locally extendable * globally revised * available in web-space on web-time * cross-linked The realization of this vision requires three interlocking components, which are: * Standards - access methods and formats need to be published and openly available * Tools - standards based tools must be readily available * Content - commonly used terminologies have to be available for access and download Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: LexGrid (RRID:SCR_006627) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/hisat2/index.shtml

Graph-based alignment of next generation sequencing reads to a population of genomes.

Proper citation: HISAT2 (RRID:SCR_015530) Copy   

•   Source: SciCrunch Registry

http://www.iu.edu/~beca/

Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version.

Proper citation: BECA (RRID:SCR_015846) Copy   

•   Source: SciCrunch Registry

http://www.genesigdb.org

Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service.

Proper citation: GeneSigDB (RRID:SCR_013275) Copy   

•   Source: SciCrunch Registry

http://www.i2b2.org

i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System. The i2b2 Center is developing a scalable informatics framework that will enable clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origin. For some resources (e.g. software) the use of the resource requires accepting a specific (e.g. OpenSource) license.

Proper citation: Informatics for Integrating Biology and the Bedside (RRID:SCR_013629) Copy   

•   Source: SciCrunch Registry